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Arsenic in PDB 3hbz: Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution, PDB code: 3hbz was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.75 / 2.05
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.551, 94.551, 107.812, 90.00, 90.00, 120.00
R / Rfree (%) 15.9 / 19.1

Other elements in 3hbz:

The structure of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution (pdb code 3hbz). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution, PDB code: 3hbz:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 3hbz

Go back to Arsenic Binding Sites List in 3hbz
Arsenic binding site 1 out of 2 in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As5

b:50.4
occ:0.80
AS A:CAC5 0.0 50.4 0.8
O2 A:CAC5 1.7 50.8 0.8
O1 A:CAC5 1.7 44.0 0.8
C1 A:CAC5 1.9 43.0 0.8
C2 A:CAC5 2.0 40.8 0.8
CA A:CA2 3.5 51.2 0.8
O A:HOH586 3.5 38.9 1.0
O A:PHE101 3.7 24.1 1.0
N A:LYS103 4.0 24.4 1.0
CA A:TRP102 4.5 21.6 1.0
O A:LYS103 4.5 30.4 1.0
CE3 A:TRP102 4.6 27.8 1.0
C A:PHE101 4.7 23.0 1.0
C A:TRP102 4.8 23.3 1.0
CB A:LYS103 4.8 26.8 1.0
CA A:LYS103 4.9 26.3 1.0

Arsenic binding site 2 out of 2 in 3hbz

Go back to Arsenic Binding Sites List in 3hbz
Arsenic binding site 2 out of 2 in the Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of A Putative Glycoside Hydrolase (BT_2081) From Bacteroides Thetaiotaomicron Vpi-5482 at 2.05 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As6

b:54.0
occ:0.60
AS A:CAC6 0.0 54.0 0.6
O1 A:CAC6 1.7 36.6 0.6
O2 A:CAC6 1.8 53.6 0.6
C1 A:CAC6 2.0 49.1 0.6
C2 A:CAC6 2.0 40.5 0.6
O A:HOH508 3.7 38.0 1.0
OG1 A:THR48 3.9 29.3 1.0
O A:HOH565 4.0 54.1 1.0
CB A:ASN49 4.0 30.8 1.0
OE1 A:GLN128 4.0 53.6 1.0
N A:ASN50 4.1 25.9 1.0
OD1 A:ASN50 4.2 46.7 1.0
N A:ASN49 4.2 27.0 1.0
CB A:THR48 4.3 26.3 1.0
CA A:ASN49 4.5 29.4 1.0
CB A:ASN50 4.6 27.1 1.0
O A:HOH493 4.6 42.3 1.0
C A:ASN49 4.7 28.9 1.0
CG A:ASN50 4.9 43.3 1.0
CA A:ASN50 4.9 28.6 1.0
CD A:GLN128 4.9 45.2 1.0
O A:HOH487 4.9 27.3 1.0
NE2 A:GLN128 5.0 36.9 1.0
OH A:TYR130 5.0 25.2 1.0

Reference:

A.P.Yeh, P.Abdubek, T.Astakhova, H.L.Axelrod, C.Bakolitsa, X.Cai, D.Carlton, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, K.Ellrott, C.L.Farr, J.Feuerhelm, J.C.Grant, A.Grzechnik, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, A.Kumar, W.W.Lam, D.Marciano, D.Mcmullan, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, C.Puckett, R.Reyes, H.J.Tien, C.B.Trame, H.Van Den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Structure of Bacteroides Thetaiotaomicron BT2081 at 2.05 A Resolution: the First Structural Representative of A New Protein Family That May Play A Role in Carbohydrate Metabolism. Acta Crystallogr.,Sect.F V. 66 1287 2010.
ISSN: ESSN 1744-3091
PubMed: 20944224
DOI: 10.1107/S1744309110028228
Page generated: Tue Oct 27 16:50:21 2020

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